- Whole genome sequencing has fundamentally changed the way microbiological food hazards in the U.S. are detected, identified and monitored, according to a blog post written by two top scientists at the U.S. Food and Drug Administration. In the post, Steven Musser and Eric L. Stevens explained that the technology is "rapid, precise, cost-effective, easy-to-use, and can be applied universally to all foodborne pathogens."
- The FDA has been a leader in the use of whole-genome sequencing, which can identify the type and source of bacteria that spoil food and cause outbreaks of illness. In 2012, the agency launched GenomeTrakr, a now-international network of laboratories that sequences microbial foodborne pathogens and uploads the data to a common public database in real time.
- "Already, GenomeTrakr has collected more than 142,000 sequenced strains, has made them freely available to anyone in the world, and continues to demonstrate how a large database of this kind is being used effectively for food safety within the United States and throughout the world," Musser and Stevens wrote.
Whole-genome sequencing, according to the FDA, "essentially reveals the genetic fingerprint of a pathogen by sequencing the chemical building blocks that make up its DNA. For example, it was recently used to help match samples of soft cheese to the genetic fingerprint of listeria monocytogenes involved in a deadly foodborne illness outbreak in early March."
Expansion of the GenomeTrakr network has helped speed up this identification of pathogens. Previously, matching a pathogen to a food source and then tracking back to identify those who may have been sickened has been a notoriously slow and painstaking step for epidemiologists trying to solve outbreaks.
A study published last year comparing two nut butter outbreaks revealed what the researchers called the "huge public health consequences" of the technology. In 2009, a salmonella outbreak linked to peanut butter killed nine people. At least 714 people in 46 states — half of them children — were sickened, and 23% were hospitalized.
A similar event in 2014, after FDA started using whole-genome sequencing to help with outbreak investigations, caused five people to report related illnesses. The latter outbreak benefited from early intervention by regulatory authorities, the study found, and resulted in significantly fewer illnesses and only one reported hospitalization.
The FDA hopes that other countries now using whole-genome sequencing will share their data with GenomeTrakr. The agency has a goal of including developing countries as they're able to join. As of July, the system consisted of 15 federal labs, 25 state health and university labs, one U.S. hospital lab, two other labs located in the U.S., 20 labs located outside of the U.S., and collaborations with independent academic researchers.
The technology is also evolving. FDA labs test new genome sequencers to see whether they are faster, better and cheaper, or maybe more mobile. Some very small sequencers available today can fit in a pocket, and FDA envisions one day having a "lab in a briefcase" so staffers can go out and do field testing.
It's easy to see how greater availability and coordination of whole-genome sequencing data could help identify the source and extent of outbreaks more quickly so fewer people around the world get sick from preventable foodborne illnesses. This could benefit manufacturers, who can suffer great blows to their reputation if the effects of an outbreak linger too long and sicken a large number of people.